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I've been looking for spells that have no upper limit damage based on caster level for my Warlock use with his Craft Staff feat.

For example, Flame Strike (Clr 5/Drd 4) has the upper limit of 15d6 damage at caster level 15. However, Hammer of Righteousness (Sanctified 2, BoED 100) cause 1d6/1d8(if evil) damage per caster level with no upper limit.

Is there any other spells, regardless of class, level and number of targets, that have infinite damage progression with caster levels?

Probably the most useful spell for your purposes is the 4th-level sorcerer-only spell wings of flurry [evoc] (Races of the Dragon 119) that is considered by some broken because of its uncapped damage and its ability to hit a great many targets at once. Another factor may be that the spell also dazes those who fail the Reflex saving throw against it. It's a nasty spell.

Also of interest may be the 3rd-level cleric spell venomfire [trans] (Serpent Kingdoms 158) that's one of the game's nastiest spells, and by my estimate routinely house-ruled to be more reasonable or banned outright. The spell causes the subject's "venom to become caustic, dealing an additional 1d6 points of acid damage per caster level with each use," therefore enabling some creatures to deal damage with it multiple times per turn. Exploiting the spell's effect becomes a matter of finding a way to poison one's attacks, like by using the collar of venom (Book of Vile Darkness 114) (50,000 gp; 3 lbs.). (Also see this answer on "Use feats to spit in a 15-ft. cone an injury poison that's linked to a poisonous bite.")

Any of them, if you take the Reserves of Strength feat from Dragonlance Campaign Setting.

Reserves of Strength has two effects:

1. You can add +1, +2, or +3 to your caster level for a single spell, but get stunned for a number of rounds equal to the bonus you choose to add. This is a bad trade most of the time, unless you are immune to stun. (If you are immune to stun, you take that many d6s in damage, instead. This is a great trade.)



2. 
   

   
   

   You can exceed the normal level-fixed limits of a spell with this feat

   
   

   
   
   

   Nothing says you have to use the first part of the feat, that is, make the CL-for-stun trade, in order to activate the second part. The closest it comes to saying that is “with this feat,” but that is not nearly sufficient to mandate making the trade—after all, simply having the feat means you are casting any spell “with this feat.” Reserves of Strength is not a metamagic feat, so it doesn’t get applied to particular spells.

   
   
   

   Furthermore, it does not say the bonuses from this feat, specifically, can exceed these limits—it says you can, “with this feat,” i.e. by virtue of having this feat. That means that it exceeding those limits is in no way limited to the bonus you choose (or not) to add to your caster level—you still get to exceed those bonuses. The feat lists a 9th-level wizard casting fireball with caster level 12th and dealing 12d6 damage, but nothing in the feat says that a 12th-level wizard, casting a CL 12th fireball, would not also deal 12d6 damage—or that a 20th-level wizard would not deal 20d6 damage. It says you exceed the limits, no ifs, ands, or buts, so that’s what you do.

   
   

And Reserves of Strength works perfectly well with spells cast from a staff:

Staffs use the spell trigger activation method, so casting a spell from a staff is usually a standard action that doesn’t provoke attacks of opportunity.

You are casting a spell “from a staff,” therefore the fact that “you can exceed the normal level-fixed limits of a spell with this feat,” applies to this spell as well as any other. Clearly, you must be the one responsible for the spell, since (barring an intelligent staff), the staff is not spending a standard action or risking an attack of opportunity.

Without Reserves of Strength

As for the more direct question of spells that have no cap to begin with, they are rare and mostly high-level. Even then, I suspect those that do exist are probably mistakes (almost-certainly the case with any lower-level spells). Certainly, the two than HeyICanChan lists, wings of flurry and venomfire, are deeply problematic spells.

Anyway, I am not aware of any resource that lists all of them, nor is this an attribute of spells that is often listed separately for searching. That would make it very difficult to compile such a list, and for the most part people don’t care—if their caster level is so high, they probably have Reserves of Strength anyway (and it’s probably a theoretical-optimization exercise to begin with). I’ll add a list if I find one, but I suspect that I will not.

In addition to the other answers here, Maw of Chaos (Spell Compendium p. 140) is a 9th-level spell with no caster level damage limit. It is also an area spell (rendering counter-options like Spell Turning nonfunctional) and deals untyped damage (so it cannot be resisted).

All spells that deal damage are to be capped as described on pages 35 and 36 of the Adjudicating Magic section of the DMG

The maximum allowed damage is either 20 or 25 dice of damage for a 9th level spell (less for lower level effects) depending on area or single target, arcane or divine.

Some take this as authoritative, while others note that it is conjoined with the new spell creation guidelines, and thus do not take it as rules.

In either case, as specific overrides general, if the spell states it is limitless, then it is. It is worth noting that this does not apply to non-damaging spells. It is also worth noting that even if not taken as rules, it is definite general guidance, popularly referred to as "Rules As Intended (RAI)".